The present invention relates generally to a method and apparatus for improved signal-to-noise ratios in mass spectrometry. The present invention is primarily directed to dissociating background ions for reducing chemical noise.
Developments in mass spectrometry (MS) technology over the past two decades have led to astonishing improvements in the sensitivity for peptide analysis. Gygi, S. P.; Aebersold, R. Curr Opin Chem Biol 2000, 4, 489-494; Chalmers, M. J.; Gaskell, S. J. Curr Opin Biotechnol 2000, 11, 384-390; Papac, D. I.; Shahrokh, Z.; Pharm Res 2001, 8, 131-145. This success is attributable to the introduction and refinement of matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI), enhancements of the efficiency and performance of mass analyzers, improvements in spectral analysis tools, as well as optimization of sample handling techniques. These developments have advanced MS to the level of a tool of choice for protein identification and characterization.
Currently, the practical limit in sensitivity is usually imposed by background ions in the mass spectrum rather than the inherent sensitivity of the mass spectrometer. For example, inspection of mass spectra obtained in the inventors"" MALDI/ESI-QqTOF and MALDI/ESI-ion trap instruments (Krutchinsky, A. N.; Zhang, W.; Chait, B. T. J Am Soc Mass Spectrom 2000, 11, 493-504; Krutchinsky, A. N.; Kalkum, M.; Chait, B. T. xe2x80x9cRapid, Automatic Identification of proteins With a Novel MALDI-Ion Trap Mass Spectrometerxe2x80x9d accepted for publication in Anal. Chem.) reveal background ion peaks at essentially every m/z value. Close examination of these individual background peaks indicates the presence of a large number of different ion species at each m/z value. Although the presence of this xe2x80x9cchemical noisexe2x80x9d is widely recognized and numerous attempts have been made to reduce its effect, its nature and origin is presently unknown. Livadaris, V.; Blais, J. -C.; Tabet, J-C. Eur. J. Mass Spectrom. 2000, 6, 409-413; Ramsey, R. S.; Goeringer, D. E.; McLuckey, S. A. Anal Chem 1993, 65, 3521-3524; Mordehai, A. V.; J. D. Henion Rapid Commun. Mass Spectrom 1993, 7, 1131-1135; Aebi, B.; Henion, J Rapid Commun. Mass Spectrom. 1996, 10, 947-951; Voyksner, R. D.; Lee H. Rapid Commun Mass Spectrom 1999, 13, 1427-1437; Guevremont, R.; Barnett, D. A.; Purves, R. W.; Vandermey, J. Anal Chem, 2000, 72, 4577-4584; Karas M, Gluckmann M, Schafer J. J Mass Spectrom 2000, 35, 1-12; Keller, B. O.; Li, L. J. Am. Soc. Mass Spectrom. 2000, 11, 88-93.
When the magnitude of the signal from analyte ions becomes comparable to that of background ions, the ion peaks of interest begin to merge with the noise and can no longer be distinguished unless special accommodations are made to increase the signal-to-noise ratio. One approach is to accumulate the spectra for longer times. However, the statistical improvement of the signal-to-noise increases rather slowly with accumulation time, and the increased time for MS analysis quickly leads to the problem of premature consumption of the sample before the full analysis can be completed. This problem is especially true for multiple MS/MS measurements of the components of peptide mixtures. Another approach for overcoming the noise limitation utilizes linked scan modes of operation. Schwartz, J. C.; Wade, A. P.; Enke, C. G.; Cooks, R. G. Anal Chem 1990, 62, 1809-1818; Thomson, B. A.; Chernushevich, I. V. Rapid Commun Mass Spectrom 1998, 12, 1323-1329; Wells, M. J.; Cooks, G. R Rapid Commun Mass Spectrom 1999, 13, 752-754. Unfortunately, current realizations of this technique have low efficiency due to the low duty cycle incurred by the necessity to scan the mass spectrometer. Although selective MS/MS analysis of the ions of interest can greatly improve the duty cycle, the m/z ratio of the ion to be fragmented may be unknown.
Accordingly there is a need for reducing chemical noise in MS experimentation.
In one embodiment, the invention relates to a method for increasing the signal-to-noise ratio in a range of mass-to-charge ratios of a mass spectrum. The method comprises generating ions of interest and background ions having mass-to-charge ratios within the range of mass-to-charge ratios. The ions of interest and the background ions are then subjected to an activation energy sufficient to cause dissociation of background ions to an extent greater than the dissociation of the ions of interest. The dissociation of the background ions causes the background ions to have mass-to-charge ratios that fall outside of the range of mass-to-charge ratios. The mass-to-charge ratios of the ions of interest are then detected.
In another embodiment, the present invention relates to an improved mass spectrometer. The mass spectrometer comprises a source of ions of interest and background ions, a mass-to-charge analyzer, and a means to transport the ions from the source to the analyzer. The mass spectrometer produces a mass spectrum of signals representing the ions of interest and the background ions in a selected range of mass-to-charge ratios. The improvement relates to providing the mass spectrometer with a means to subject the ions of interest and the background ions to an activation energy sufficient to cause dissociation of background ions to an extent greater than the dissociation of the ions of interest. The dissociation of the background ions causes the background ions to have mass-to-charge ratios that fall outside of the range of selected mass-to-charge ratios which increases the ratio of signal-to-noise in the selected range of mass-to-charge ratios.